This is the pathway enrichment analysis practical of the OBDS course
The first part of this pracical is using gprofiler to perform ORA on output dataset of differentially expressed genes from DESeq2
The major aim of this exercise is to get you used to reading online tool documentation and playing with different paramters.
# load librarys
library(tidyverse)## ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.2 ──
## ✔ ggplot2 3.4.0 ✔ purrr 0.3.5
## ✔ tibble 3.1.8 ✔ dplyr 1.0.10
## ✔ tidyr 1.2.1 ✔ stringr 1.4.1
## ✔ readr 2.1.3 ✔ forcats 0.5.2
## ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
## ✖ dplyr::filter() masks stats::filter()
## ✖ dplyr::lag() masks stats::lag()library(gprofiler2)# read in results table we output from DESeq2 this morning using tidyverse read_csv()
all_genes_df <- read.csv("~/OBDS_training/pathway_analysis/data/CD8_vs_CD4_DE_results_lfcshrinkage.csv")
dim(all_genes_df)## [1] 22535 9# check its dimensions - and look at the top of the file -> what does this tell us about our table?
# dim = 22,535 -> this contains all genes -> need to filter to get those tested We want to perform a classic Over representation analsis (ORA) using gprofiler - to do this we first need to create our gene subsets
# Subset 1 - All genes tested in differential expression (this is our background/control gene list) - i.e. remove padj == NA
all_genes_tested_df <- all_genes_df[!is.na(all_genes_df$padj), ]
dim(all_genes_tested_df)## [1] 17729 9# Subset 2 - All sig upregulated genes (padj < 0.05. & log2FoldChange > 1)
upreg_genes_df <- all_genes_tested_df[all_genes_tested_df$padj< 0.05 & all_genes_tested_df$log2FoldChange> 1, ]
# Subset 3 - All sig downregulated genes (padj < 0.05. & log2FoldChange < 1)
downreg_genes_df <- all_genes_tested_df[all_genes_tested_df$padj < 0.05 & all_genes_tested_df$log2FoldChange< -1, ]
# Check the dimensions of each of your dataframes using dim()
dim(downreg_genes_df)## [1] 1204 9dim(upreg_genes_df)## [1] 915 9# all_genes_df_filtered should be 17729
# upreg_genes_df should be 915
# downreg_genes_df should be 1204# from each of these dataframes get a vector of the ensembl ids
all_gene_ids <- all_genes_tested_df$ensembl_gene_ids
upreg_gene_ids <- upreg_genes_df$ensembl_gene_ids
downreg_gene_ids <- downreg_genes_df$ensembl_gene_ids#Perform ORA using g:profiler
# use the gost() function - what parameters should we include/change??
# we want to test the ORA of upreg_gene_ids vs our all_gene_ids
# get help for function
# write query and assign to output variable named `gost_results_obj`
gost_results_obj <- gost(
query = upreg_gene_ids,
organism = "mmusculus",
exclude_iea = TRUE,
correction_method = c("g_SCS"),
custom_bg = all_gene_ids,
)## Detected custom background input, domain scope is set to 'custom'gost_results_obj$result## query significant p_value term_size query_size intersection_size
## 1 query_1 TRUE 5.832954e-03 3 910 3
## 2 query_1 TRUE 2.241023e-02 4 910 3
## 3 query_1 TRUE 2.025637e-90 1156 910 255
## 4 query_1 TRUE 3.442480e-87 1966 910 330
## 5 query_1 TRUE 2.393765e-63 121 910 77
## 6 query_1 TRUE 2.051786e-54 367 910 116
## 7 query_1 TRUE 3.264559e-52 5351 910 508
## 8 query_1 TRUE 7.223250e-52 488 910 130
## 9 query_1 TRUE 1.041558e-51 251 910 95
## 10 query_1 TRUE 1.592447e-51 252 910 95
## 11 query_1 TRUE 1.655828e-51 258 910 96
## 12 query_1 TRUE 6.818270e-51 1064 910 193
## 13 query_1 TRUE 3.402025e-49 697 910 152
## 14 query_1 TRUE 9.610473e-49 83 910 57
## 15 query_1 TRUE 3.740459e-48 95 910 60
## 16 query_1 TRUE 4.377013e-48 393 910 113
## 17 query_1 TRUE 4.456446e-48 119 910 66
## 18 query_1 TRUE 9.691044e-48 970 910 179
## 19 query_1 TRUE 9.691044e-48 970 910 179
## 20 query_1 TRUE 2.880241e-47 539 910 131
## 21 query_1 TRUE 6.427681e-47 127 910 67
## 22 query_1 TRUE 1.170943e-46 996 910 180
## 23 query_1 TRUE 1.424216e-46 1775 910 250
## 24 query_1 TRUE 7.408844e-46 1080 910 187
## 25 query_1 TRUE 1.285341e-45 307 910 98
## 26 query_1 TRUE 1.290913e-45 834 910 162
## 27 query_1 TRUE 3.472691e-45 908 910 169
## 28 query_1 TRUE 3.598452e-45 133 910 67
## 29 query_1 TRUE 3.644339e-45 95 910 58
## 30 query_1 TRUE 1.176163e-44 219 910 83
## 31 query_1 TRUE 1.859302e-44 295 910 95
## 32 query_1 TRUE 2.071558e-44 97 910 58
## 33 query_1 TRUE 2.876977e-44 233 910 85
## 34 query_1 TRUE 2.703847e-43 481 910 119
## 35 query_1 TRUE 3.103659e-43 771 910 152
## 36 query_1 TRUE 1.535757e-42 538 910 125
## 37 query_1 TRUE 8.948207e-42 706 910 143
## 38 query_1 TRUE 4.652295e-40 1639 910 227
## 39 query_1 TRUE 6.087544e-40 558 910 124
## 40 query_1 TRUE 6.396966e-40 721 910 142
## 41 query_1 TRUE 1.349359e-39 1176 910 186
## 42 query_1 TRUE 2.105455e-39 195 910 74
## 43 query_1 TRUE 2.820957e-39 592 910 127
## 44 query_1 TRUE 3.217089e-39 245 910 82
## 45 query_1 TRUE 5.309777e-39 300 910 90
## 46 query_1 TRUE 5.744456e-39 169 910 69
## 47 query_1 TRUE 2.672814e-38 334 910 94
## 48 query_1 TRUE 2.009723e-37 3344 910 348
## 49 query_1 TRUE 3.787815e-36 489 910 111
## 50 query_1 TRUE 5.783813e-36 173 910 67
## 51 query_1 TRUE 1.000575e-35 387 910 98
## 52 query_1 TRUE 1.022499e-35 152 910 63
## 53 query_1 TRUE 1.033109e-35 1802 910 232
## 54 query_1 TRUE 1.218687e-35 169 910 66
## 55 query_1 TRUE 2.663062e-35 399 910 99
## 56 query_1 TRUE 3.592637e-35 3647 910 363
## 57 query_1 TRUE 3.925450e-35 309 910 87
## 58 query_1 TRUE 2.861754e-34 3695 910 364
## 59 query_1 TRUE 1.594773e-33 163 910 63
## 60 query_1 TRUE 6.517451e-33 351 910 90
## 61 query_1 TRUE 5.342864e-31 2803 910 296
## 62 query_1 TRUE 1.165500e-25 438 910 91
## 63 query_1 TRUE 3.830997e-23 4463 910 383
## 64 query_1 TRUE 5.684916e-23 2656 910 266
## 65 query_1 TRUE 1.317282e-22 4489 910 383
## 66 query_1 TRUE 1.688126e-19 4056 910 347
## 67 query_1 TRUE 3.688854e-16 7731 910 545
## 68 query_1 TRUE 1.319515e-14 7350 910 519
## 69 query_1 TRUE 1.999731e-13 1066 910 126
## 70 query_1 TRUE 2.685495e-13 1134 910 131
## 71 query_1 TRUE 4.862063e-13 12579 910 770
## 72 query_1 TRUE 2.395391e-12 645 910 89
## 73 query_1 TRUE 4.723526e-12 1161 910 130
## 74 query_1 TRUE 9.331910e-11 696 910 90
## 75 query_1 TRUE 1.477003e-10 471 910 70
## 76 query_1 TRUE 1.877524e-10 680 910 88
## 77 query_1 TRUE 2.070010e-10 2881 910 243
## 78 query_1 TRUE 2.491115e-10 6963 910 481
## 79 query_1 TRUE 4.816747e-10 1999 910 184
## 80 query_1 TRUE 5.578550e-10 201 910 42
## 81 query_1 TRUE 1.346141e-09 916 910 105
## 82 query_1 TRUE 2.939841e-09 347 910 56
## 83 query_1 TRUE 5.703578e-09 859 910 99
## 84 query_1 TRUE 6.391425e-09 272 910 48
## 85 query_1 TRUE 6.468373e-09 4401 910 330
## 86 query_1 TRUE 1.425667e-08 133 910 32
## 87 query_1 TRUE 1.525539e-08 158 910 35
## 88 query_1 TRUE 1.871882e-08 373 910 57
## 89 query_1 TRUE 1.871882e-08 373 910 57
## 90 query_1 TRUE 1.975494e-08 1156 910 120
## 91 query_1 TRUE 2.741647e-08 313 910 51
## 92 query_1 TRUE 4.031172e-08 163 910 35
## 93 query_1 TRUE 4.345869e-08 2296 910 197
## 94 query_1 TRUE 4.531376e-08 2718 910 224
## 95 query_1 TRUE 4.633992e-08 237 910 43
## 96 query_1 TRUE 5.236201e-08 182 910 37
## 97 query_1 TRUE 5.780609e-08 210 910 40
## 98 query_1 TRUE 6.359995e-08 220 910 41
## 99 query_1 TRUE 1.189919e-07 1805 910 163
## 100 query_1 TRUE 1.230066e-07 2697 910 221
## 101 query_1 TRUE 3.162857e-07 202 910 38
## 102 query_1 TRUE 4.590392e-07 59 910 20
## 103 query_1 TRUE 4.738735e-07 15 910 11
## 104 query_1 TRUE 4.837624e-07 12 910 10
## 105 query_1 TRUE 4.837624e-07 12 910 10
## 106 query_1 TRUE 4.837624e-07 12 910 10
## 107 query_1 TRUE 5.040220e-07 205 910 38
## 108 query_1 TRUE 6.189067e-07 1812 910 161
## 109 query_1 TRUE 6.764621e-07 798 910 89
## 110 query_1 TRUE 7.683690e-07 352 910 52
## 111 query_1 TRUE 7.776615e-07 477 910 63
## 112 query_1 TRUE 9.984716e-07 399 910 56
## 113 query_1 TRUE 1.133256e-06 3740 910 281
## 114 query_1 TRUE 1.245799e-06 768 910 86
## 115 query_1 TRUE 1.299266e-06 90 910 24
## 116 query_1 TRUE 1.303499e-06 335 910 50
## 117 query_1 TRUE 1.429006e-06 2877 910 228
## 118 query_1 TRUE 1.443889e-06 16 910 11
## 119 query_1 TRUE 1.447407e-06 98 910 25
## 120 query_1 TRUE 1.493669e-06 44 910 17
## 121 query_1 TRUE 2.384251e-06 1242 910 120
## 122 query_1 TRUE 3.084771e-06 1247 910 120
## 123 query_1 TRUE 3.765581e-06 1096 910 109
## 124 query_1 TRUE 3.857494e-06 851 910 91
## 125 query_1 TRUE 3.880582e-06 3216 910 247
## 126 query_1 TRUE 4.620974e-06 3009 910 234
## 127 query_1 TRUE 6.352809e-06 587 910 70
## 128 query_1 TRUE 6.391031e-06 2552 910 205
## 129 query_1 TRUE 8.928150e-06 579 910 69
## 130 query_1 TRUE 9.531991e-06 506 910 63
## 131 query_1 TRUE 1.099026e-05 76 910 21
## 132 query_1 TRUE 1.474430e-05 463 910 59
## 133 query_1 TRUE 1.502419e-05 229 910 38
## 134 query_1 TRUE 1.586874e-05 50 910 17
## 135 query_1 TRUE 1.713753e-05 109 910 25
## 136 query_1 TRUE 1.945984e-05 231 910 38
## 137 query_1 TRUE 2.023218e-05 71 910 20
## 138 query_1 TRUE 2.548141e-05 1994 910 167
## 139 query_1 TRUE 3.072275e-05 583 910 68
## 140 query_1 TRUE 3.371419e-05 485 910 60
## 141 query_1 TRUE 3.684121e-05 66 910 19
## 142 query_1 TRUE 4.159712e-05 105 910 24
## 143 query_1 TRUE 5.176378e-05 47 910 16
## 144 query_1 TRUE 5.935304e-05 2032 910 168
## 145 query_1 TRUE 6.274372e-05 133 910 27
## 146 query_1 TRUE 6.329281e-05 4031 910 290
## 147 query_1 TRUE 6.581978e-05 684 910 75
## 148 query_1 TRUE 6.619349e-05 61 910 18
## 149 query_1 TRUE 6.826781e-05 531 910 63
## 150 query_1 TRUE 8.383314e-05 597 910 68
## 151 query_1 TRUE 8.750879e-05 2027 910 167
## 152 query_1 TRUE 9.496596e-05 586 910 67
## 153 query_1 TRUE 1.044101e-04 85 910 21
## 154 query_1 TRUE 1.080225e-04 1190 910 111
## 155 query_1 TRUE 1.102722e-04 745 910 79
## 156 query_1 TRUE 1.240299e-04 1728 910 147
## 157 query_1 TRUE 1.313587e-04 86 910 21
## 158 query_1 TRUE 1.435816e-04 71 910 19
## 159 query_1 TRUE 1.563165e-04 64 910 18
## 160 query_1 TRUE 2.040152e-04 715 910 76
## 161 query_1 TRUE 2.415842e-04 2308 910 183
## 162 query_1 TRUE 2.497061e-04 123 910 25
## 163 query_1 TRUE 3.041920e-04 2299 910 182
## 164 query_1 TRUE 3.372744e-04 288 910 41
## 165 query_1 TRUE 3.412663e-04 223 910 35
## 166 query_1 TRUE 3.777226e-04 34 910 13
## 167 query_1 TRUE 4.796912e-04 136 910 26
## 168 query_1 TRUE 4.990232e-04 61 910 17
## 169 query_1 TRUE 5.719788e-04 35 910 13
## 170 query_1 TRUE 6.547243e-04 400 910 50
## 171 query_1 TRUE 6.567548e-04 388 910 49
## 172 query_1 TRUE 6.587471e-04 48 910 15
## 173 query_1 TRUE 7.754969e-04 1396 910 122
## 174 query_1 TRUE 8.136357e-04 130 910 25
## 175 query_1 TRUE 8.762489e-04 753 910 77
## 176 query_1 TRUE 8.919594e-04 253 910 37
## 177 query_1 TRUE 9.082526e-04 404 910 50
## 178 query_1 TRUE 9.163083e-04 392 910 49
## 179 query_1 TRUE 1.076388e-03 2483 910 191
## 180 query_1 TRUE 1.156705e-03 407 910 50
## 181 query_1 TRUE 1.206915e-03 745 910 76
## 182 query_1 TRUE 1.361077e-03 257 910 37
## 183 query_1 TRUE 1.482991e-03 338 910 44
## 184 query_1 TRUE 1.482991e-03 338 910 44
## 185 query_1 TRUE 1.655469e-03 226 910 34
## 186 query_1 TRUE 1.841379e-03 9 910 7
## 187 query_1 TRUE 1.860759e-03 32 910 12
## 188 query_1 TRUE 1.956599e-03 3515 910 252
## 189 query_1 TRUE 2.061555e-03 700 910 72
## 190 query_1 TRUE 2.267661e-03 156 910 27
## 191 query_1 TRUE 2.294943e-03 343 910 44
## 192 query_1 TRUE 2.324280e-03 240 910 35
## 193 query_1 TRUE 2.516252e-03 263 910 37
## 194 query_1 TRUE 2.589496e-03 480 910 55
## 195 query_1 TRUE 2.654869e-03 393 910 48
## 196 query_1 TRUE 2.783988e-03 33 910 12
## 197 query_1 TRUE 3.318875e-03 722 910 73
## 198 query_1 TRUE 3.513677e-03 348 910 44
## 199 query_1 TRUE 3.535035e-03 190 910 30
## 200 query_1 TRUE 3.541536e-03 409 910 49
## 201 query_1 TRUE 3.611723e-03 1005 910 93
## 202 query_1 TRUE 3.635083e-03 397 910 48
## 203 query_1 TRUE 4.188245e-03 202 910 31
## 204 query_1 TRUE 4.469868e-03 151 910 26
## 205 query_1 TRUE 4.809657e-03 647 910 67
## 206 query_1 TRUE 4.941914e-03 634 910 66
## 207 query_1 TRUE 5.204163e-03 123 910 23
## 208 query_1 TRUE 5.204163e-03 123 910 23
## 209 query_1 TRUE 5.552641e-03 663 910 68
## 210 query_1 TRUE 5.565819e-03 543 910 59
## 211 query_1 TRUE 5.974078e-03 1045 910 95
## 212 query_1 TRUE 6.057618e-03 29 910 11
## 213 query_1 TRUE 6.600620e-03 206 910 31
## 214 query_1 TRUE 6.862475e-03 332 910 42
## 215 query_1 TRUE 7.154337e-03 7 910 6
## 216 query_1 TRUE 7.496231e-03 419 910 49
## 217 query_1 TRUE 7.559325e-03 4379 910 299
## 218 query_1 TRUE 7.630545e-03 286 910 38
## 219 query_1 TRUE 9.419010e-03 50 910 14
## 220 query_1 TRUE 1.093351e-02 189 910 29
## 221 query_1 TRUE 1.154326e-02 759 910 74
## 222 query_1 TRUE 1.164971e-02 279 910 37
## 223 query_1 TRUE 1.200554e-02 1284 910 110
## 224 query_1 TRUE 1.232118e-02 327 910 41
## 225 query_1 TRUE 1.274683e-02 25 910 10
## 226 query_1 TRUE 1.286751e-02 110 910 21
## 227 query_1 TRUE 1.289665e-02 257 910 35
## 228 query_1 TRUE 1.404014e-02 492 910 54
## 229 query_1 TRUE 1.636075e-02 121 910 22
## 230 query_1 TRUE 1.768452e-02 431 910 49
## 231 query_1 TRUE 2.141011e-02 346 910 42
## 232 query_1 TRUE 2.481238e-02 760 910 73
## 233 query_1 TRUE 2.495971e-02 78 910 17
## 234 query_1 TRUE 2.630882e-02 186 910 28
## 235 query_1 TRUE 2.733076e-02 8 910 6
## 236 query_1 TRUE 2.788370e-02 33 910 11
## 237 query_1 TRUE 3.115642e-02 1158 910 100
## 238 query_1 TRUE 3.494453e-02 340 910 41
## 239 query_1 TRUE 3.495387e-02 63 910 15
## 240 query_1 TRUE 3.499827e-02 1621 910 130
## 241 query_1 TRUE 3.508815e-02 1161 910 100
## 242 query_1 TRUE 3.649999e-02 1162 910 100
## 243 query_1 TRUE 4.085555e-02 1532 910 124
## 244 query_1 TRUE 4.432100e-02 368 910 43
## 245 query_1 TRUE 4.514519e-02 331 910 40
## 246 query_1 TRUE 4.534886e-02 471 910 51
## 247 query_1 TRUE 4.557239e-02 458 910 50
## 248 query_1 TRUE 4.577544e-02 688 910 67
## 249 query_1 TRUE 4.605813e-02 236 910 32
## 250 query_1 TRUE 4.668286e-02 17 910 8
## 251 query_1 TRUE 4.945704e-02 214 910 30
## 252 query_1 TRUE 7.915622e-73 883 910 203
## 253 query_1 TRUE 1.175285e-69 1055 910 218
## 254 query_1 TRUE 3.075209e-59 408 910 127
## 255 query_1 TRUE 3.775106e-57 83 910 62
## 256 query_1 TRUE 3.521837e-54 79 910 59
## 257 query_1 TRUE 3.645920e-54 2883 910 350
## 258 query_1 TRUE 4.649234e-54 3135 910 368
## 259 query_1 TRUE 1.944937e-53 693 910 157
## 260 query_1 TRUE 1.989245e-53 576 910 143
## 261 query_1 TRUE 1.192071e-29 4591 910 409
## 262 query_1 TRUE 1.620688e-13 12523 910 769
## 263 query_1 TRUE 5.959685e-12 713 910 94
## 264 query_1 TRUE 5.995499e-11 11102 910 695
## 265 query_1 TRUE 1.189524e-10 663 910 87
## 266 query_1 TRUE 1.329217e-06 241 910 41
## 267 query_1 TRUE 2.693162e-06 1330 910 126
## 268 query_1 TRUE 1.864085e-05 1240 910 117
## 269 query_1 TRUE 2.080348e-03 741 910 75
## 270 query_1 TRUE 2.733076e-02 8 910 6
## 271 query_1 TRUE 3.030997e-54 82 910 60
## 272 query_1 TRUE 1.023202e-49 131 910 70
## 273 query_1 TRUE 4.820958e-23 978 910 139
## 274 query_1 TRUE 3.405408e-14 475 910 77
## 275 query_1 TRUE 3.405408e-14 475 910 77
## 276 query_1 TRUE 2.440607e-13 368 910 65
## 277 query_1 TRUE 7.695264e-09 18 910 13
## 278 query_1 TRUE 7.546917e-07 103 910 26
## 279 query_1 TRUE 2.137040e-05 6386 910 426
## 280 query_1 TRUE 5.618606e-05 7 910 7
## 281 query_1 TRUE 3.873988e-04 144 910 27
## 282 query_1 TRUE 7.154337e-03 7 910 6
## 283 query_1 TRUE 2.036351e-02 5 910 5
## 284 query_1 TRUE 4.977558e-02 8097 910 498
## 285 query_1 TRUE 4.536963e-08 69 910 21
## 286 query_1 TRUE 3.284042e-06 93 910 22
## 287 query_1 TRUE 7.652162e-06 97 910 22
## 288 query_1 TRUE 1.392567e-04 62 910 16
## 289 query_1 TRUE 3.792133e-03 822 910 75
## 290 query_1 TRUE 4.008578e-03 106 910 19
## 291 query_1 TRUE 5.213270e-03 311 910 37
## 292 query_1 TRUE 8.294157e-03 394 910 43
## 293 query_1 TRUE 1.221935e-02 7 910 5
## 294 query_1 TRUE 2.048357e-02 292 910 34
## 295 query_1 TRUE 4.076467e-02 380 910 40
## 296 query_1 TRUE 4.776694e-02 94 910 16
## 297 query_1 TRUE 1.953474e-14 79 910 28
## 298 query_1 TRUE 3.514514e-09 44 910 17
## 299 query_1 TRUE 3.921882e-08 44 910 16
## 300 query_1 TRUE 1.217971e-07 47 910 16
## 301 query_1 TRUE 1.885391e-07 42 910 15
## 302 query_1 TRUE 5.637518e-07 18 910 10
## 303 query_1 TRUE 2.810751e-05 37 910 12
## 304 query_1 TRUE 2.810751e-05 37 910 12
## 305 query_1 TRUE 3.539132e-05 150 910 25
## 306 query_1 TRUE 3.922907e-05 182 910 28
## 307 query_1 TRUE 5.180607e-05 69 910 16
## 308 query_1 TRUE 5.245244e-05 61 910 15
## 309 query_1 TRUE 1.045546e-04 138 910 23
## 310 query_1 TRUE 2.052165e-04 94 910 18
## 311 query_1 TRUE 2.332183e-04 68 910 15
## 312 query_1 TRUE 2.700338e-04 115 910 20
## 313 query_1 TRUE 3.090274e-04 61 910 14
## 314 query_1 TRUE 5.969630e-04 73 910 15
## 315 query_1 TRUE 6.170792e-04 48 910 12
## 316 query_1 TRUE 6.452071e-04 153 910 23
## 317 query_1 TRUE 2.909147e-03 145 910 21
## 318 query_1 TRUE 4.429432e-03 33 910 9
## 319 query_1 TRUE 7.754236e-03 70 910 13
## 320 query_1 TRUE 1.268988e-02 104 910 16
## 321 query_1 TRUE 1.430819e-02 30 910 8
## 322 query_1 TRUE 2.454266e-02 99 910 15
## 323 query_1 TRUE 2.644574e-02 193 910 23
## 324 query_1 TRUE 2.663226e-02 5689 910 350
## 325 query_1 TRUE 4.556924e-02 151 910 19
## 326 query_1 TRUE 3.679020e-02 24 910 7
## 327 query_1 TRUE 7.745029e-52 81 910 57
## 328 query_1 TRUE 1.056949e-51 78 910 56
## 329 query_1 TRUE 1.553224e-51 69 910 53
## 330 query_1 TRUE 4.622996e-51 86 910 58
## 331 query_1 TRUE 1.005040e-49 89 910 58
## 332 query_1 TRUE 1.421775e-49 148 910 72
## 333 query_1 TRUE 3.406379e-49 70 910 52
## 334 query_1 TRUE 6.939491e-49 77 910 54
## 335 query_1 TRUE 4.143923e-48 72 910 52
## 336 query_1 TRUE 8.378349e-47 85 910 55
## 337 query_1 TRUE 1.198324e-45 77 910 52
## 338 query_1 TRUE 3.608468e-45 89 910 55
## 339 query_1 TRUE 9.096294e-44 85 910 53
## 340 query_1 TRUE 1.101256e-43 157 910 69
## 341 query_1 TRUE 6.007007e-43 91 910 54
## 342 query_1 TRUE 1.311545e-42 88 910 53
## 343 query_1 TRUE 7.998747e-36 140 910 59
## 344 query_1 TRUE 3.002327e-34 121 910 54
## 345 query_1 TRUE 2.394363e-33 158 910 60
## 346 query_1 TRUE 2.916395e-31 784 910 132
## 347 query_1 TRUE 3.040915e-29 134 910 52
## 348 query_1 TRUE 1.219461e-28 463 910 95
## 349 query_1 TRUE 8.248232e-27 173 910 56
## 350 query_1 TRUE 1.366628e-25 1326 910 169
## 351 query_1 TRUE 7.788159e-21 655 910 102
## 352 query_1 TRUE 5.364922e-12 542 910 75
## 353 query_1 TRUE 4.123970e-08 120 910 27
## 354 query_1 TRUE 2.719836e-07 402 910 53
## 355 query_1 TRUE 2.826127e-07 148 910 29
## 356 query_1 TRUE 4.289012e-07 7 910 7
## 357 query_1 TRUE 4.465165e-06 6422 910 420
## 358 query_1 TRUE 6.081574e-06 308 910 42
## 359 query_1 TRUE 4.470739e-05 10 910 7
## 360 query_1 TRUE 4.470739e-05 10 910 7
## 361 query_1 TRUE 6.953745e-05 30 910 11
## 362 query_1 TRUE 1.090472e-04 67 910 16
## 363 query_1 TRUE 1.191179e-04 294 910 38
## 364 query_1 TRUE 2.606949e-04 55 910 14
## 365 query_1 TRUE 2.954687e-03 4 910 4
## 366 query_1 TRUE 4.941637e-03 44 910 11
## 367 query_1 TRUE 8.157146e-03 18 910 7
## 368 query_1 TRUE 1.434040e-02 1609 910 121
## 369 query_1 TRUE 2.876857e-02 101 910 16
## 370 query_1 TRUE 5.778639e-07 2819 910 226
## 371 query_1 TRUE 6.534371e-05 4358 910 309
## 372 query_1 TRUE 2.318664e-03 3118 910 228
## 373 query_1 TRUE 3.062145e-03 5810 910 382
## 374 query_1 TRUE 3.588231e-03 4225 910 292
## 375 query_1 TRUE 5.943124e-03 4351 910 298
## 376 query_1 TRUE 7.144697e-03 1668 910 136
## 377 query_1 TRUE 1.405161e-02 8217 910 508
## 378 query_1 TRUE 3.469737e-07 115 910 24
## 379 query_1 TRUE 1.435710e-06 72 910 18
## 380 query_1 TRUE 6.571595e-05 3226 910 227
## 381 query_1 TRUE 2.149496e-04 39 910 11
## 382 query_1 TRUE 1.067052e-03 142 910 21
## 383 query_1 TRUE 1.515108e-03 47 910 11
## 384 query_1 TRUE 5.935056e-03 54 910 11
## 385 query_1 TRUE 2.510516e-02 152 910 19
## 386 query_1 TRUE 4.692050e-02 9 910 4
## precision recall term_id source
## 1 0.003296703 1.00000000 CORUM:2900 CORUM
## 2 0.003296703 0.75000000 CORUM:2742 CORUM
## 3 0.280219780 0.22058824 GO:0006955 GO:BP
## 4 0.362637363 0.16785351 GO:0002376 GO:BP
## 5 0.084615385 0.63636364 GO:0050853 GO:BP
## 6 0.127472527 0.31607629 GO:0002443 GO:BP
## 7 0.558241758 0.09493553 GO:0050896 GO:BP
## 8 0.142857143 0.26639344 GO:0045087 GO:BP
## 9 0.104395604 0.37848606 GO:0002429 GO:BP
## 10 0.104395604 0.37698413 GO:0002757 GO:BP
## 11 0.105494505 0.37209302 GO:0002768 GO:BP
## 12 0.212087912 0.18139098 GO:0006952 GO:BP
## 13 0.167032967 0.21807747 GO:0098542 GO:BP
## 14 0.062637363 0.68674699 GO:0006958 GO:BP
## 15 0.065934066 0.63157895 GO:0006910 GO:BP
## 16 0.124175824 0.28753181 GO:0002764 GO:BP
## 17 0.072527473 0.55462185 GO:0006911 GO:BP
## 18 0.196703297 0.18453608 GO:0043207 GO:BP
## 19 0.196703297 0.18453608 GO:0051707 GO:BP
## 20 0.143956044 0.24304267 GO:0002252 GO:BP
## 21 0.073626374 0.52755906 GO:0099024 GO:BP
## 22 0.197802198 0.18072289 GO:0009607 GO:BP
## 23 0.274725275 0.14084507 GO:0009605 GO:BP
## 24 0.205494505 0.17314815 GO:0044419 GO:BP
## 25 0.107692308 0.31921824 GO:0002253 GO:BP
## 26 0.178021978 0.19424460 GO:0045321 GO:BP
## 27 0.185714286 0.18612335 GO:0001775 GO:BP
## 28 0.073626374 0.50375940 GO:0010324 GO:BP
## 29 0.063736264 0.61052632 GO:0002455 GO:BP
## 30 0.091208791 0.37899543 GO:0050851 GO:BP
## 31 0.104395604 0.32203390 GO:0002449 GO:BP
## 32 0.063736264 0.59793814 GO:0006956 GO:BP
## 33 0.093406593 0.36480687 GO:0042742 GO:BP
## 34 0.130769231 0.24740125 GO:0050778 GO:BP
## 35 0.167032967 0.19714656 GO:0002684 GO:BP
## 36 0.137362637 0.23234201 GO:0009617 GO:BP
## 37 0.157142857 0.20254958 GO:0050776 GO:BP
## 38 0.249450549 0.13849908 GO:0048584 GO:BP
## 39 0.136263736 0.22222222 GO:0002694 GO:BP
## 40 0.156043956 0.19694868 GO:0046649 GO:BP
## 41 0.204395604 0.15816327 GO:0002682 GO:BP
## 42 0.081318681 0.37948718 GO:0050864 GO:BP
## 43 0.139560440 0.21452703 GO:0050865 GO:BP
## 44 0.090109890 0.33469388 GO:0006909 GO:BP
## 45 0.098901099 0.30000000 GO:0042113 GO:BP
## 46 0.075824176 0.40828402 GO:0006959 GO:BP
## 47 0.103296703 0.28143713 GO:0002250 GO:BP
## 48 0.382417582 0.10406699 GO:0007165 GO:BP
## 49 0.121978022 0.22699387 GO:0051249 GO:BP
## 50 0.073626374 0.38728324 GO:0019724 GO:BP
## 51 0.107692308 0.25322997 GO:0002696 GO:BP
## 52 0.069230769 0.41447368 GO:0050871 GO:BP
## 53 0.254945055 0.12874584 GO:0007166 GO:BP
## 54 0.072527473 0.39053254 GO:0016064 GO:BP
## 55 0.108791209 0.24812030 GO:0050867 GO:BP
## 56 0.398901099 0.09953386 GO:0023052 GO:BP
## 57 0.095604396 0.28155340 GO:0002460 GO:BP
## 58 0.400000000 0.09851150 GO:0007154 GO:BP
## 59 0.069230769 0.38650307 GO:0008037 GO:BP
## 60 0.098901099 0.25641026 GO:0051251 GO:BP
## 61 0.325274725 0.10560114 GO:0048583 GO:BP
## 62 0.100000000 0.20776256 GO:0006897 GO:BP
## 63 0.420879121 0.08581672 GO:0051716 GO:BP
## 64 0.292307692 0.10015060 GO:0006950 GO:BP
## 65 0.420879121 0.08531967 GO:0048518 GO:BP
## 66 0.381318681 0.08555227 GO:0048522 GO:BP
## 67 0.598901099 0.07049541 GO:0065007 GO:BP
## 68 0.570329670 0.07061224 GO:0050789 GO:BP
## 69 0.138461538 0.11819887 GO:0016477 GO:BP
## 70 0.143956044 0.11552028 GO:0016192 GO:BP
## 71 0.846153846 0.06121313 GO:0008150 GO:BP
## 72 0.097802198 0.13798450 GO:0061024 GO:BP
## 73 0.142857143 0.11197244 GO:0048870 GO:BP
## 74 0.098901099 0.12931034 GO:0032101 GO:BP
## 75 0.076923077 0.14861996 GO:0006954 GO:BP
## 76 0.096703297 0.12941176 GO:0022603 GO:BP
## 77 0.267032967 0.08434571 GO:0048731 GO:BP
## 78 0.528571429 0.06907942 GO:0050794 GO:BP
## 79 0.202197802 0.09204602 GO:0051239 GO:BP
## 80 0.046153846 0.20895522 GO:0002703 GO:BP
## 81 0.115384615 0.11462882 GO:0040011 GO:BP
## 82 0.061538462 0.16138329 GO:0032103 GO:BP
## 83 0.108791209 0.11525029 GO:0007155 GO:BP
## 84 0.052747253 0.17647059 GO:0050900 GO:BP
## 85 0.362637363 0.07498296 GO:0032501 GO:BP
## 86 0.035164835 0.24060150 GO:0001906 GO:BP
## 87 0.038461538 0.22151899 GO:0030595 GO:BP
## 88 0.062637363 0.15281501 GO:0006935 GO:BP
## 89 0.062637363 0.15281501 GO:0042330 GO:BP
## 90 0.131868132 0.10380623 GO:0051240 GO:BP
## 91 0.056043956 0.16293930 GO:0002697 GO:BP
## 92 0.038461538 0.21472393 GO:0097529 GO:BP
## 93 0.216483516 0.08580139 GO:0048513 GO:BP
## 94 0.246153846 0.08241354 GO:0048869 GO:BP
## 95 0.047252747 0.18143460 GO:0031349 GO:BP
## 96 0.040659341 0.20329670 GO:0002274 GO:BP
## 97 0.043956044 0.19047619 GO:0060326 GO:BP
## 98 0.045054945 0.18636364 GO:0002699 GO:BP
## 99 0.179120879 0.09030471 GO:0009653 GO:BP
## 100 0.242857143 0.08194290 GO:0030154 GO:BP
## 101 0.041758242 0.18811881 GO:0045765 GO:BP
## 102 0.021978022 0.33898305 GO:0043299 GO:BP
## 103 0.012087912 0.73333333 GO:0002220 GO:BP
## 104 0.010989011 0.83333333 GO:1990858 GO:BP
## 105 0.010989011 0.83333333 GO:1990840 GO:BP
## 106 0.010989011 0.83333333 GO:0002223 GO:BP
## 107 0.041758242 0.18536585 GO:1901342 GO:BP
## 108 0.176923077 0.08885210 GO:0050793 GO:BP
## 109 0.097802198 0.11152882 GO:0048534 GO:BP
## 110 0.057142857 0.14772727 GO:0007186 GO:BP
## 111 0.069230769 0.13207547 GO:0031347 GO:BP
## 112 0.061538462 0.14035088 GO:0048514 GO:BP
## 113 0.308791209 0.07513369 GO:0048856 GO:BP
## 114 0.094505495 0.11197917 GO:0030097 GO:BP
## 115 0.026373626 0.26666667 GO:0031341 GO:BP
## 116 0.054945055 0.14925373 GO:0001525 GO:BP
## 117 0.250549451 0.07924922 GO:0006810 GO:BP
## 118 0.012087912 0.68750000 GO:0002758 GO:BP
## 119 0.027472527 0.25510204 GO:0001909 GO:BP
## 120 0.018681319 0.38636364 GO:0043300 GO:BP
## 121 0.131868132 0.09661836 GO:0010647 GO:BP
## 122 0.131868132 0.09623095 GO:0023056 GO:BP
## 123 0.119780220 0.09945255 GO:0009967 GO:BP
## 124 0.100000000 0.10693302 GO:0002520 GO:BP
## 125 0.271428571 0.07680348 GO:0007275 GO:BP
## 126 0.257142857 0.07776670 GO:0051234 GO:BP
## 127 0.076923077 0.11925043 GO:0001816 GO:BP
## 128 0.225274725 0.08032915 GO:0042221 GO:BP
## 129 0.075824176 0.11917098 GO:0098609 GO:BP
## 130 0.069230769 0.12450593 GO:0002521 GO:BP
## 131 0.023076923 0.27631579 GO:0002444 GO:BP
## 132 0.064835165 0.12742981 GO:0001568 GO:BP
## 133 0.041758242 0.16593886 GO:0002366 GO:BP
## 134 0.018681319 0.34000000 GO:0002715 GO:BP
## 135 0.027472527 0.22935780 GO:0097530 GO:BP
## 136 0.041758242 0.16450216 GO:0002263 GO:BP
## 137 0.021978022 0.28169014 GO:0001910 GO:BP
## 138 0.183516484 0.08375125 GO:0010033 GO:BP
## 139 0.074725275 0.11663808 GO:0001817 GO:BP
## 140 0.065934066 0.12371134 GO:0001944 GO:BP
## 141 0.020879121 0.28787879 GO:0030593 GO:BP
## 142 0.026373626 0.22857143 GO:0034341 GO:BP
## 143 0.017582418 0.34042553 GO:0042269 GO:BP
## 144 0.184615385 0.08267717 GO:0009966 GO:BP
## 145 0.029670330 0.20300752 GO:0071674 GO:BP
## 146 0.318681319 0.07194245 GO:0032502 GO:BP
## 147 0.082417582 0.10964912 GO:0030334 GO:BP
## 148 0.019780220 0.29508197 GO:0031343 GO:BP
## 149 0.069230769 0.11864407 GO:0010942 GO:BP
## 150 0.074725275 0.11390285 GO:0030155 GO:BP
## 151 0.183516484 0.08238777 GO:0070887 GO:BP
## 152 0.073626374 0.11433447 GO:0035239 GO:BP
## 153 0.023076923 0.24705882 GO:0071621 GO:BP
## 154 0.121978022 0.09327731 GO:0042592 GO:BP
## 155 0.086813187 0.10604027 GO:0040012 GO:BP
## 156 0.161538462 0.08506944 GO:0035556 GO:BP
## 157 0.023076923 0.24418605 GO:1990266 GO:BP
## 158 0.020879121 0.26760563 GO:0002275 GO:BP
## 159 0.019780220 0.28125000 GO:0002228 GO:BP
## 160 0.083516484 0.10629371 GO:2000145 GO:BP
## 161 0.201098901 0.07928943 GO:0023051 GO:BP
## 162 0.027472527 0.20325203 GO:0002705 GO:BP
## 163 0.200000000 0.07916485 GO:0010646 GO:BP
## 164 0.045054945 0.14236111 GO:0070661 GO:BP
## 165 0.038461538 0.15695067 GO:0070663 GO:BP
## 166 0.014285714 0.38235294 GO:0002717 GO:BP
## 167 0.028571429 0.19117647 GO:0007204 GO:BP
## 168 0.018681319 0.27868852 GO:0042267 GO:BP
## 169 0.014285714 0.37142857 GO:0036230 GO:BP
## 170 0.054945055 0.12500000 GO:0098771 GO:BP
## 171 0.053846154 0.12628866 GO:0045785 GO:BP
## 172 0.016483516 0.31250000 GO:0002886 GO:BP
## 173 0.134065934 0.08739255 GO:0008283 GO:BP
## 174 0.027472527 0.19230769 GO:0019722 GO:BP
## 175 0.084615385 0.10225764 GO:0000902 GO:BP
## 176 0.040659341 0.14624506 GO:0042060 GO:BP
## 177 0.054945055 0.12376238 GO:0050801 GO:BP
## 178 0.053846154 0.12500000 GO:0055080 GO:BP
## 179 0.209890110 0.07692308 GO:0065008 GO:BP
## 180 0.054945055 0.12285012 GO:0051345 GO:BP
## 181 0.083516484 0.10201342 GO:0072359 GO:BP
## 182 0.040659341 0.14396887 GO:0046651 GO:BP
## 183 0.048351648 0.13017751 GO:0009611 GO:BP
## 184 0.048351648 0.13017751 GO:0055065 GO:BP
## 185 0.037362637 0.15044248 GO:0032496 GO:BP
## 186 0.007692308 0.77777778 GO:0010919 GO:BP
## 187 0.013186813 0.37500000 GO:0045954 GO:BP
## 188 0.276923077 0.07169275 GO:0051179 GO:BP
## 189 0.079120879 0.10285714 GO:1902533 GO:BP
## 190 0.029670330 0.17307692 GO:0002833 GO:BP
## 191 0.048351648 0.12827988 GO:0006873 GO:BP
## 192 0.038461538 0.14583333 GO:0002237 GO:BP
## 193 0.040659341 0.14068441 GO:0032943 GO:BP
## 194 0.060439560 0.11458333 GO:0043068 GO:BP
## 195 0.052747253 0.12213740 GO:0001819 GO:BP
## 196 0.013186813 0.36363636 GO:0002548 GO:BP
## 197 0.080219780 0.10110803 GO:0035295 GO:BP
## 198 0.048351648 0.12643678 GO:0030099 GO:BP
## 199 0.032967033 0.15789474 GO:0019932 GO:BP
## 200 0.053846154 0.11980440 GO:0030335 GO:BP
## 201 0.102197802 0.09253731 GO:0051094 GO:BP
## 202 0.052747253 0.12090680 GO:1903131 GO:BP
## 203 0.034065934 0.15346535 GO:0050670 GO:BP
## 204 0.028571429 0.17218543 GO:0002706 GO:BP
## 205 0.073626374 0.10355487 GO:0046903 GO:BP
## 206 0.072527473 0.10410095 GO:0051336 GO:BP
## 207 0.025274725 0.18699187 GO:0045766 GO:BP
## 208 0.025274725 0.18699187 GO:1904018 GO:BP
## 209 0.074725275 0.10256410 GO:0034097 GO:BP
## 210 0.064835165 0.10865562 GO:0000165 GO:BP
## 211 0.104395604 0.09090909 GO:2000026 GO:BP
## 212 0.012087912 0.37931034 GO:0042119 GO:BP
## 213 0.034065934 0.15048544 GO:0032944 GO:BP
## 214 0.046153846 0.12650602 GO:0030003 GO:BP
## 215 0.006593407 0.85714286 GO:0060732 GO:BP
## 216 0.053846154 0.11694511 GO:2000147 GO:BP
## 217 0.328571429 0.06828043 GO:0016043 GO:BP
## 218 0.041758242 0.13286713 GO:0002831 GO:BP
## 219 0.015384615 0.28000000 GO:0001912 GO:BP
## 220 0.031868132 0.15343915 GO:0002573 GO:BP
## 221 0.081318681 0.09749671 GO:0048646 GO:BP
## 222 0.040659341 0.13261649 GO:0006875 GO:BP
## 223 0.120879121 0.08566978 GO:0010941 GO:BP
## 224 0.045054945 0.12538226 GO:0007159 GO:BP
## 225 0.010989011 0.40000000 GO:0043302 GO:BP
## 226 0.023076923 0.19090909 GO:0050729 GO:BP
## 227 0.038461538 0.13618677 GO:0050727 GO:BP
## 228 0.059340659 0.10975610 GO:0043408 GO:BP
## 229 0.024175824 0.18181818 GO:0045089 GO:BP
## 230 0.053846154 0.11368910 GO:0040017 GO:BP
## 231 0.046153846 0.12138728 GO:0043410 GO:BP
## 232 0.080219780 0.09605263 GO:0051241 GO:BP
## 233 0.018681319 0.21794872 GO:0042100 GO:BP
## 234 0.030769231 0.15053763 GO:0045088 GO:BP
## 235 0.006593407 0.75000000 GO:0002576 GO:BP
## 236 0.012087912 0.33333333 GO:0070098 GO:BP
## 237 0.109890110 0.08635579 GO:0043067 GO:BP
## 238 0.045054945 0.12058824 GO:0002683 GO:BP
## 239 0.016483516 0.23809524 GO:0034109 GO:BP
## 240 0.142857143 0.08019741 GO:0071310 GO:BP
## 241 0.109890110 0.08613264 GO:1902531 GO:BP
## 242 0.109890110 0.08605852 GO:0042127 GO:BP
## 243 0.136263736 0.08093995 GO:0048468 GO:BP
## 244 0.047252747 0.11684783 GO:0048871 GO:BP
## 245 0.043956044 0.12084592 GO:0003013 GO:BP
## 246 0.056043956 0.10828025 GO:0043065 GO:BP
## 247 0.054945055 0.10917031 GO:0051046 GO:BP
## 248 0.073626374 0.09738372 GO:0045597 GO:BP
## 249 0.035164835 0.13559322 GO:0072507 GO:BP
## 250 0.008791209 0.47058824 GO:0002495 GO:BP
## 251 0.032967033 0.14018692 GO:0072503 GO:BP
## 252 0.223076923 0.22989807 GO:0005615 GO:CC
## 253 0.239560440 0.20663507 GO:0005576 GO:CC
## 254 0.139560440 0.31127451 GO:0009897 GO:CC
## 255 0.068131868 0.74698795 GO:0019814 GO:CC
## 256 0.064835165 0.74683544 GO:0042571 GO:CC
## 257 0.384615385 0.12140132 GO:0005886 GO:CC
## 258 0.404395604 0.11738437 GO:0071944 GO:CC
## 259 0.172527473 0.22655123 GO:0009986 GO:CC
## 260 0.157142857 0.24826389 GO:0098552 GO:CC
## 261 0.449450549 0.08908734 GO:0016020 GO:CC
## 262 0.845054945 0.06140701 GO:0005575 GO:CC
## 263 0.103296703 0.13183731 GO:0031226 GO:CC
## 264 0.763736264 0.06260133 GO:0110165 GO:CC
## 265 0.095604396 0.13122172 GO:0005887 GO:CC
## 266 0.045054945 0.17012448 GO:0043235 GO:CC
## 267 0.138461538 0.09473684 GO:0031224 GO:CC
## 268 0.128571429 0.09435484 GO:0016021 GO:CC
## 269 0.082417582 0.10121457 GO:0098590 GO:CC
## 270 0.006593407 0.75000000 GO:0042613 GO:CC
## 271 0.065934066 0.73170732 GO:0034987 GO:MF
## 272 0.076923077 0.53435115 GO:0003823 GO:MF
## 273 0.152747253 0.14212679 GO:0005102 GO:MF
## 274 0.084615385 0.16210526 GO:0060089 GO:MF
## 275 0.084615385 0.16210526 GO:0038023 GO:MF
## 276 0.071428571 0.17663043 GO:0004888 GO:MF
## 277 0.014285714 0.72222222 GO:0023023 GO:MF
## 278 0.028571429 0.25242718 GO:0140375 GO:MF
## 279 0.468131868 0.06670842 GO:0005515 GO:MF
## 280 0.007692308 1.00000000 GO:0032394 GO:MF
## 281 0.029670330 0.18750000 GO:0004930 GO:MF
## 282 0.006593407 0.85714286 GO:0023024 GO:MF
## 283 0.005494505 1.00000000 GO:0031726 GO:MF
## 284 0.547252747 0.06150426 GO:0005488 GO:MF
## 285 0.023076923 0.30434783 HP:0001287 HP
## 286 0.024175824 0.23655914 HP:0011450 HP
## 287 0.024175824 0.22680412 HP:0032158 HP
## 288 0.017582418 0.25806452 HP:0002633 HP
## 289 0.082417582 0.09124088 HP:0025142 HP
## 290 0.020879121 0.17924528 HP:0000988 HP
## 291 0.040659341 0.11897106 HP:0001945 HP
## 292 0.047252747 0.10913706 HP:0004370 HP
## 293 0.005494505 0.71428571 HP:0004444 HP
## 294 0.037362637 0.11643836 HP:0012378 HP
## 295 0.043956044 0.10526316 HP:0001744 HP
## 296 0.017582418 0.17021277 HP:0025337 HP
## 297 0.030769231 0.35443038 KEGG:04640 KEGG
## 298 0.018681319 0.38636364 KEGG:05332 KEGG
## 299 0.017582418 0.36363636 KEGG:05330 KEGG
## 300 0.017582418 0.34042553 KEGG:04940 KEGG
## 301 0.016483516 0.35714286 KEGG:05320 KEGG
## 302 0.010989011 0.55555556 KEGG:05310 KEGG
## 303 0.013186813 0.32432432 KEGG:05150 KEGG
## 304 0.013186813 0.32432432 KEGG:04672 KEGG
## 305 0.027472527 0.16666667 KEGG:04062 KEGG
## 306 0.030769231 0.15384615 KEGG:04060 KEGG
## 307 0.017582418 0.23188406 KEGG:04612 KEGG
## 308 0.016483516 0.24590164 KEGG:04061 KEGG
## 309 0.025274725 0.16666667 KEGG:04145 KEGG
## 310 0.019780220 0.19148936 KEGG:04650 KEGG
## 311 0.016483516 0.22058824 KEGG:05140 KEGG
## 312 0.021978022 0.17391304 KEGG:04514 KEGG
## 313 0.015384615 0.22950820 KEGG:05416 KEGG
## 314 0.016483516 0.20547945 KEGG:04662 KEGG
## 315 0.013186813 0.25000000 KEGG:05144 KEGG
## 316 0.025274725 0.15032680 KEGG:05152 KEGG
## 317 0.023076923 0.14482759 KEGG:05202 KEGG
## 318 0.009890110 0.27272727 KEGG:05340 KEGG
## 319 0.014285714 0.18571429 KEGG:05323 KEGG
## 320 0.017582418 0.15384615 KEGG:05145 KEGG
## 321 0.008791209 0.26666667 KEGG:05143 KEGG
## 322 0.016483516 0.15151515 KEGG:04625 KEGG
## 323 0.025274725 0.11917098 KEGG:05169 KEGG
## 324 0.384615385 0.06152224 KEGG:00000 KEGG
## 325 0.020879121 0.12582781 KEGG:04020 KEGG
## 326 0.007692308 0.29166667 MIRNA:mmu-miR-27b-3p MIRNA
## 327 0.062637363 0.70370370 REAC:R-MMU-2168880 REAC
## 328 0.061538462 0.71794872 REAC:R-MMU-2029481 REAC
## 329 0.058241758 0.76811594 REAC:R-MMU-5690714 REAC
## 330 0.063736264 0.67441860 REAC:R-MMU-983695 REAC
## 331 0.063736264 0.65168539 REAC:R-MMU-2173782 REAC
## 332 0.079120879 0.48648649 REAC:R-MMU-198933 REAC
## 333 0.057142857 0.74285714 REAC:R-MMU-173623 REAC
## 334 0.059340659 0.70129870 REAC:R-MMU-2730905 REAC
## 335 0.057142857 0.72222222 REAC:R-MMU-166786 REAC
## 336 0.060439560 0.64705882 REAC:R-MMU-2029485 REAC
## 337 0.057142857 0.67532468 REAC:R-MMU-166663 REAC
## 338 0.060439560 0.61797753 REAC:R-MMU-2871809 REAC
## 339 0.058241758 0.62352941 REAC:R-MMU-977606 REAC
## 340 0.075824176 0.43949045 REAC:R-MMU-202733 REAC
## 341 0.059340659 0.59340659 REAC:R-MMU-2871796 REAC
## 342 0.058241758 0.60227273 REAC:R-MMU-166658 REAC
## 343 0.064835165 0.42142857 REAC:R-MMU-2029480 REAC
## 344 0.059340659 0.44628099 REAC:R-MMU-2029482 REAC
## 345 0.065934066 0.37974684 REAC:R-MMU-983705 REAC
## 346 0.145054945 0.16836735 REAC:R-MMU-168249 REAC
## 347 0.057142857 0.38805970 REAC:R-MMU-2871837 REAC
## 348 0.104395604 0.20518359 REAC:R-MMU-109582 REAC
## 349 0.061538462 0.32369942 REAC:R-MMU-2454202 REAC
## 350 0.185714286 0.12745098 REAC:R-MMU-168256 REAC
## 351 0.112087912 0.15572519 REAC:R-MMU-1280218 REAC
## 352 0.082417582 0.13837638 REAC:R-MMU-5653656 REAC
## 353 0.029670330 0.22500000 REAC:R-MMU-373076 REAC
## 354 0.058241758 0.13184080 REAC:R-MMU-6798695 REAC
## 355 0.031868132 0.19594595 REAC:R-MMU-500792 REAC
## 356 0.007692308 1.00000000 REAC:R-MMU-1247673 REAC
## 357 0.461538462 0.06540019 REAC:0000000 REAC
## 358 0.046153846 0.13636364 REAC:R-MMU-372790 REAC
## 359 0.007692308 0.70000000 REAC:R-MMU-1237044 REAC
## 360 0.007692308 0.70000000 REAC:R-MMU-1480926 REAC
## 361 0.012087912 0.36666667 REAC:R-MMU-380108 REAC
## 362 0.017582418 0.23880597 REAC:R-MMU-375276 REAC
## 363 0.041758242 0.12925170 REAC:R-MMU-388396 REAC
## 364 0.015384615 0.25454545 REAC:R-MMU-2172127 REAC
## 365 0.004395604 1.00000000 REAC:R-MMU-6799990 REAC
## 366 0.012087912 0.25000000 REAC:R-MMU-2424491 REAC
## 367 0.007692308 0.38888889 REAC:R-MMU-6803157 REAC
## 368 0.132967033 0.07520199 REAC:R-MMU-162582 REAC
## 369 0.017582418 0.15841584 REAC:R-MMU-416476 REAC
## 370 0.248351648 0.08017027 TF:M01172 TF
## 371 0.339560440 0.07090408 TF:M01808_1 TF
## 372 0.250549451 0.07312380 TF:M00658 TF
## 373 0.419780220 0.06574871 TF:M00749 TF
## 374 0.320879121 0.06911243 TF:M07107_1 TF
## 375 0.327472527 0.06849000 TF:M10270 TF
## 376 0.149450549 0.08153477 TF:M00192_1 TF
## 377 0.558241758 0.06182305 TF:M00646 TF
## 378 0.026373626 0.20869565 WP:WP1396 WP
## 379 0.019780220 0.25000000 WP:WP189 WP
## 380 0.249450549 0.07036578 WP:000000 WP
## 381 0.012087912 0.28205128 WP:WP3626 WP
## 382 0.023076923 0.14788732 WP:WP2292 WP
## 383 0.012087912 0.23404255 WP:WP3632 WP
## 384 0.012087912 0.20370370 WP:WP3625 WP
## 385 0.020879121 0.12500000 WP:WP85 WP
## 386 0.004395604 0.44444444 WP:WP2271 WP
## term_name
## 1 PLC-gamma-2-Lab-Blnk complex, BCR stimulated
## 2 Gata2-Tal1-Tcf3-Lmo2 complex
## 3 immune response
## 4 immune system process
## 5 B cell receptor signaling pathway
## 6 leukocyte mediated immunity
## 7 response to stimulus
## 8 innate immune response
## 9 immune response-activating cell surface receptor signaling pathway
## 10 immune response-activating signal transduction
## 11 immune response-regulating cell surface receptor signaling pathway
## 12 defense response
## 13 defense response to other organism
## 14 complement activation, classical pathway
## 15 phagocytosis, recognition
## 16 immune response-regulating signaling pathway
## 17 phagocytosis, engulfment
## 18 response to external biotic stimulus
## 19 response to other organism
## 20 immune effector process
## 21 plasma membrane invagination
## 22 response to biotic stimulus
## 23 response to external stimulus
## 24 biological process involved in interspecies interaction between organisms
## 25 activation of immune response
## 26 leukocyte activation
## 27 cell activation
## 28 membrane invagination
## 29 humoral immune response mediated by circulating immunoglobulin
## 30 antigen receptor-mediated signaling pathway
## 31 lymphocyte mediated immunity
## 32 complement activation
## 33 defense response to bacterium
## 34 positive regulation of immune response
## 35 positive regulation of immune system process
## 36 response to bacterium
## 37 regulation of immune response
## 38 positive regulation of response to stimulus
## 39 regulation of leukocyte activation
## 40 lymphocyte activation
## 41 regulation of immune system process
## 42 regulation of B cell activation
## 43 regulation of cell activation
## 44 phagocytosis
## 45 B cell activation
## 46 humoral immune response
## 47 adaptive immune response
## 48 signal transduction
## 49 regulation of lymphocyte activation
## 50 B cell mediated immunity
## 51 positive regulation of leukocyte activation
## 52 positive regulation of B cell activation
## 53 cell surface receptor signaling pathway
## 54 immunoglobulin mediated immune response
## 55 positive regulation of cell activation
## 56 signaling
## 57 adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains
## 58 cell communication
## 59 cell recognition
## 60 positive regulation of lymphocyte activation
## 61 regulation of response to stimulus
## 62 endocytosis
## 63 cellular response to stimulus
## 64 response to stress
## 65 positive regulation of biological process
## 66 positive regulation of cellular process
## 67 biological regulation
## 68 regulation of biological process
## 69 cell migration
## 70 vesicle-mediated transport
## 71 biological_process
## 72 membrane organization
## 73 cell motility
## 74 regulation of response to external stimulus
## 75 inflammatory response
## 76 regulation of anatomical structure morphogenesis
## 77 system development
## 78 regulation of cellular process
## 79 regulation of multicellular organismal process
## 80 regulation of leukocyte mediated immunity
## 81 locomotion
## 82 positive regulation of response to external stimulus
## 83 cell adhesion
## 84 leukocyte migration
## 85 multicellular organismal process
## 86 cell killing
## 87 leukocyte chemotaxis
## 88 chemotaxis
## 89 taxis
## 90 positive regulation of multicellular organismal process
## 91 regulation of immune effector process
## 92 myeloid leukocyte migration
## 93 animal organ development
## 94 cellular developmental process
## 95 positive regulation of defense response
## 96 myeloid leukocyte activation
## 97 cell chemotaxis
## 98 positive regulation of immune effector process
## 99 anatomical structure morphogenesis
## 100 cell differentiation
## 101 regulation of angiogenesis
## 102 leukocyte degranulation
## 103 innate immune response activating cell surface receptor signaling pathway
## 104 cellular response to lectin
## 105 response to lectin
## 106 stimulatory C-type lectin receptor signaling pathway
## 107 regulation of vasculature development
## 108 regulation of developmental process
## 109 hematopoietic or lymphoid organ development
## 110 G protein-coupled receptor signaling pathway
## 111 regulation of defense response
## 112 blood vessel morphogenesis
## 113 anatomical structure development
## 114 hemopoiesis
## 115 regulation of cell killing
## 116 angiogenesis
## 117 transport
## 118 innate immune response-activating signal transduction
## 119 leukocyte mediated cytotoxicity
## 120 regulation of leukocyte degranulation
## 121 positive regulation of cell communication
## 122 positive regulation of signaling
## 123 positive regulation of signal transduction
## 124 immune system development
## 125 multicellular organism development
## 126 establishment of localization
## 127 cytokine production
## 128 response to chemical
## 129 cell-cell adhesion
## 130 leukocyte differentiation
## 131 myeloid leukocyte mediated immunity
## 132 blood vessel development
## 133 leukocyte activation involved in immune response
## 134 regulation of natural killer cell mediated immunity
## 135 granulocyte migration
## 136 cell activation involved in immune response
## 137 regulation of leukocyte mediated cytotoxicity
## 138 response to organic substance
## 139 regulation of cytokine production
## 140 vasculature development
## 141 neutrophil chemotaxis
## 142 response to interferon-gamma
## 143 regulation of natural killer cell mediated cytotoxicity
## 144 regulation of signal transduction
## 145 mononuclear cell migration
## 146 developmental process
## 147 regulation of cell migration
## 148 positive regulation of cell killing
## 149 positive regulation of cell death
## 150 regulation of cell adhesion
## 151 cellular response to chemical stimulus
## 152 tube morphogenesis
## 153 granulocyte chemotaxis
## 154 homeostatic process
## 155 regulation of locomotion
## 156 intracellular signal transduction
## 157 neutrophil migration
## 158 myeloid cell activation involved in immune response
## 159 natural killer cell mediated immunity
## 160 regulation of cell motility
## 161 regulation of signaling
## 162 positive regulation of leukocyte mediated immunity
## 163 regulation of cell communication
## 164 leukocyte proliferation
## 165 regulation of leukocyte proliferation
## 166 positive regulation of natural killer cell mediated immunity
## 167 positive regulation of cytosolic calcium ion concentration
## 168 natural killer cell mediated cytotoxicity
## 169 granulocyte activation
## 170 inorganic ion homeostasis
## 171 positive regulation of cell adhesion
## 172 regulation of myeloid leukocyte mediated immunity
## 173 cell population proliferation
## 174 calcium-mediated signaling
## 175 cell morphogenesis
## 176 wound healing
## 177 ion homeostasis
## 178 cation homeostasis
## 179 regulation of biological quality
## 180 positive regulation of hydrolase activity
## 181 circulatory system development
## 182 lymphocyte proliferation
## 183 response to wounding
## 184 metal ion homeostasis
## 185 response to lipopolysaccharide
## 186 regulation of inositol phosphate biosynthetic process
## 187 positive regulation of natural killer cell mediated cytotoxicity
## 188 localization
## 189 positive regulation of intracellular signal transduction
## 190 positive regulation of response to biotic stimulus
## 191 cellular ion homeostasis
## 192 response to molecule of bacterial origin
## 193 mononuclear cell proliferation
## 194 positive regulation of programmed cell death
## 195 positive regulation of cytokine production
## 196 monocyte chemotaxis
## 197 tube development
## 198 myeloid cell differentiation
## 199 second-messenger-mediated signaling
## 200 positive regulation of cell migration
## 201 positive regulation of developmental process
## 202 mononuclear cell differentiation
## 203 regulation of lymphocyte proliferation
## 204 regulation of lymphocyte mediated immunity
## 205 secretion
## 206 regulation of hydrolase activity
## 207 positive regulation of angiogenesis
## 208 positive regulation of vasculature development
## 209 response to cytokine
## 210 MAPK cascade
## 211 regulation of multicellular organismal development
## 212 neutrophil activation
## 213 regulation of mononuclear cell proliferation
## 214 cellular cation homeostasis
## 215 positive regulation of inositol phosphate biosynthetic process
## 216 positive regulation of cell motility
## 217 cellular component organization
## 218 regulation of response to biotic stimulus
## 219 positive regulation of leukocyte mediated cytotoxicity
## 220 myeloid leukocyte differentiation
## 221 anatomical structure formation involved in morphogenesis
## 222 cellular metal ion homeostasis
## 223 regulation of cell death
## 224 leukocyte cell-cell adhesion
## 225 positive regulation of leukocyte degranulation
## 226 positive regulation of inflammatory response
## 227 regulation of inflammatory response
## 228 regulation of MAPK cascade
## 229 positive regulation of innate immune response
## 230 positive regulation of locomotion
## 231 positive regulation of MAPK cascade
## 232 negative regulation of multicellular organismal process
## 233 B cell proliferation
## 234 regulation of innate immune response
## 235 platelet degranulation
## 236 chemokine-mediated signaling pathway
## 237 regulation of programmed cell death
## 238 negative regulation of immune system process
## 239 homotypic cell-cell adhesion
## 240 cellular response to organic substance
## 241 regulation of intracellular signal transduction
## 242 regulation of cell population proliferation
## 243 cell development
## 244 multicellular organismal homeostasis
## 245 circulatory system process
## 246 positive regulation of apoptotic process
## 247 regulation of secretion
## 248 positive regulation of cell differentiation
## 249 divalent inorganic cation homeostasis
## 250 antigen processing and presentation of peptide antigen via MHC class II
## 251 cellular divalent inorganic cation homeostasis
## 252 extracellular space
## 253 extracellular region
## 254 external side of plasma membrane
## 255 immunoglobulin complex
## 256 immunoglobulin complex, circulating
## 257 plasma membrane
## 258 cell periphery
## 259 cell surface
## 260 side of membrane
## 261 membrane
## 262 cellular_component
## 263 intrinsic component of plasma membrane
## 264 cellular anatomical entity
## 265 integral component of plasma membrane
## 266 receptor complex
## 267 intrinsic component of membrane
## 268 integral component of membrane
## 269 plasma membrane region
## 270 MHC class II protein complex
## 271 immunoglobulin receptor binding
## 272 antigen binding
## 273 signaling receptor binding
## 274 molecular transducer activity
## 275 signaling receptor activity
## 276 transmembrane signaling receptor activity
## 277 MHC protein complex binding
## 278 immune receptor activity
## 279 protein binding
## 280 MHC class Ib receptor activity
## 281 G protein-coupled receptor activity
## 282 MHC class I protein complex binding
## 283 CCR1 chemokine receptor binding
## 284 binding
## 285 Meningitis
## 286 Unusual CNS infection
## 287 Unusual infection by anatomical site
## 288 Vasculitis
## 289 Constitutional symptom
## 290 Skin rash
## 291 Fever
## 292 Abnormality of temperature regulation
## 293 Spherocytosis
## 294 Fatigue
## 295 Splenomegaly
## 296 Red eye
## 297 Hematopoietic cell lineage
## 298 Graft-versus-host disease
## 299 Allograft rejection
## 300 Type I diabetes mellitus
## 301 Autoimmune thyroid disease
## 302 Asthma
## 303 Staphylococcus aureus infection
## 304 Intestinal immune network for IgA production
## 305 Chemokine signaling pathway
## 306 Cytokine-cytokine receptor interaction
## 307 Antigen processing and presentation
## 308 Viral protein interaction with cytokine and cytokine receptor
## 309 Phagosome
## 310 Natural killer cell mediated cytotoxicity
## 311 Leishmaniasis
## 312 Cell adhesion molecules
## 313 Viral myocarditis
## 314 B cell receptor signaling pathway
## 315 Malaria
## 316 Tuberculosis
## 317 Transcriptional misregulation in cancer
## 318 Primary immunodeficiency
## 319 Rheumatoid arthritis
## 320 Toxoplasmosis
## 321 African trypanosomiasis
## 322 C-type lectin receptor signaling pathway
## 323 Epstein-Barr virus infection
## 324 KEGG root term
## 325 Calcium signaling pathway
## 326 mmu-miR-27b-3p
## 327 Scavenging of heme from plasma
## 328 FCGR activation
## 329 CD22 mediated BCR regulation
## 330 Antigen activates B Cell Receptor (BCR) leading to generation of second messengers
## 331 Binding and Uptake of Ligands by Scavenger Receptors
## 332 Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell
## 333 Classical antibody-mediated complement activation
## 334 Role of LAT2/NTAL/LAB on calcium mobilization
## 335 Creation of C4 and C2 activators
## 336 Role of phospholipids in phagocytosis
## 337 Initial triggering of complement
## 338 FCERI mediated Ca+2 mobilization
## 339 Regulation of Complement cascade
## 340 Cell surface interactions at the vascular wall
## 341 FCERI mediated MAPK activation
## 342 Complement cascade
## 343 Fcgamma receptor (FCGR) dependent phagocytosis
## 344 Regulation of actin dynamics for phagocytic cup formation
## 345 Signaling by the B Cell Receptor (BCR)
## 346 Innate Immune System
## 347 FCERI mediated NF-kB activation
## 348 Hemostasis
## 349 Fc epsilon receptor (FCERI) signaling
## 350 Immune System
## 351 Adaptive Immune System
## 352 Vesicle-mediated transport
## 353 Class A/1 (Rhodopsin-like receptors)
## 354 Neutrophil degranulation
## 355 GPCR ligand binding
## 356 Erythrocytes take up oxygen and release carbon dioxide
## 357 REACTOME root term
## 358 Signaling by GPCR
## 359 Erythrocytes take up carbon dioxide and release oxygen
## 360 O2/CO2 exchange in erythrocytes
## 361 Chemokine receptors bind chemokines
## 362 Peptide ligand-binding receptors
## 363 GPCR downstream signalling
## 364 DAP12 interactions
## 365 Metal sequestration by antimicrobial proteins
## 366 DAP12 signaling
## 367 Antimicrobial peptides
## 368 Signal Transduction
## 369 G alpha (q) signalling events
## 370 Factor: PU.1; motif: NNNNYYYACTTCCTCTTTY
## 371 Factor: NMYC; motif: CAYCTG; match class: 1
## 372 Factor: PU.1; motif: WGAGGAAG
## 373 Factor: SREBP-1; motif: CACSCCA
## 374 Factor: LXR-alpha:RXR-alpha; motif: TGACCTNNAGTRACCYNNN; match class: 1
## 375 Factor: IRF-4; motif: NAAARRGGAASTGARANN
## 376 Factor: GR; motif: NNNNNNCNNTNTGTNCTNN; match class: 1
## 377 Factor: LF-A1; motif: GGGSTCWR
## 378 GPCRs, non-odorant
## 379 GPCRs, class A rhodopsin-like
## 380 WIKIPATHWAYS
## 381 Microglia pathogen phagocytosis pathway
## 382 Chemokine signaling pathway
## 383 Lung fibrosis
## 384 Tyrobp causal network in microglia
## 385 Focal adhesion
## 386 Macrophage markers
## effective_domain_size source_order
## 1 17225 291
## 2 17225 271
## 3 17225 2884
## 4 17225 1027
## 5 17225 15352
## 6 17225 1087
## 7 17225 15390
## 8 17225 13097
## 9 17225 1073
## 10 17225 1390
## 11 17225 1401
## 12 17225 2881
## 13 17225 21964
## 14 17225 2887
## 15 17225 2846
## 16 17225 1397
## 17 17225 2847
## 18 17225 12178
## 19 17225 16036
## 20 17225 905
## 21 17225 22200
## 22 17225 3975
## 23 17225 3973
## 24 17225 12763
## 25 17225 906
## 26 17225 13197
## 27 17225 550
## 28 17225 4537
## 29 17225 1099
## 30 17225 15350
## 31 17225 1093
## 32 17225 2885
## 33 17225 11902
## 34 17225 15295
## 35 17225 1323
## 36 17225 3984
## 37 17225 15293
## 38 17225 14876
## 39 17225 1333
## 40 17225 14245
## 41 17225 1321
## 42 17225 15363
## 43 17225 15364
## 44 17225 2845
## 45 17225 11523
## 46 17225 2888
## 47 17225 903
## 48 17225 3061
## 49 17225 15684
## 50 17225 6929
## 51 17225 1335
## 52 17225 15370
## 53 17225 3062
## 54 17225 5660
## 55 17225 15366
## 56 17225 7643
## 57 17225 1104
## 58 17225 3050
## 59 17225 3499
## 60 17225 15686
## 61 17225 14875
## 62 17225 2836
## 63 17225 16044
## 64 17225 2880
## 65 17225 14820
## 66 17225 14824
## 67 17225 18589
## 68 17225 15301
## 69 17225 5812
## 70 17225 5738
## 71 17225 3526
## 72 17225 17746
## 73 17225 15139
## 74 17225 8532
## 75 17225 2883
## 76 17225 7590
## 77 17225 15011
## 78 17225 15305
## 79 17225 15677
## 80 17225 1342
## 81 17225 11442
## 82 17225 8534
## 83 17225 3051
## 84 17225 15393
## 85 17225 8794
## 86 17225 638
## 87 17225 7913
## 88 17225 2869
## 89 17225 11655
## 90 17225 15678
## 91 17225 1336
## 92 17225 21844
## 93 17225 14815
## 94 17225 15138
## 95 17225 8274
## 96 17225 927
## 97 17225 17080
## 98 17225 1338
## 99 17225 4017
## 100 17225 7711
## 101 17225 13471
## 102 17225 12211
## 103 17225 875
## 104 17225 29141
## 105 17225 29131
## 106 17225 878
## 107 17225 24635
## 108 17225 15304
## 109 17225 14834
## 110 17225 3080
## 111 17225 8272
## 112 17225 14816
## 113 17225 15126
## 114 17225 7695
## 115 17225 8266
## 116 17225 435
## 117 17225 2762
## 118 17225 1391
## 119 17225 640
## 120 17225 12212
## 121 17225 4788
## 122 17225 7647
## 123 17225 4263
## 124 17225 1163
## 125 17225 3162
## 126 17225 15672
## 127 17225 583
## 128 17225 11605
## 129 17225 21975
## 130 17225 1164
## 131 17225 1088
## 132 17225 462
## 133 17225 1019
## 134 17225 1354
## 135 17225 21845
## 136 17225 916
## 137 17225 641
## 138 17225 4303
## 139 17225 584
## 140 17225 669
## 141 17225 7912
## 142 17225 9844
## 143 17225 11626
## 144 17225 4262
## 145 17225 19633
## 146 17225 8795
## 147 17225 7808
## 148 17225 8268
## 149 17225 5059
## 150 17225 7712
## 151 17225 19091
## 152 17225 10240
## 153 17225 19587
## 154 17225 11816
## 155 17225 11443
## 156 17225 10450
## 157 17225 28899
## 158 17225 928
## 159 17225 882
## 160 17225 29352
## 161 17225 7642
## 162 17225 1344
## 163 17225 4787
## 164 17225 18970
## 165 17225 18972
## 166 17225 1356
## 167 17225 3098
## 168 17225 11624
## 169 17225 10933
## 170 17225 22062
## 171 17225 13491
## 172 17225 1518
## 173 17225 3563
## 174 17225 6928
## 175 17225 307
## 176 17225 11495
## 177 17225 15310
## 178 17225 16763
## 179 17225 18590
## 180 17225 15765
## 181 17225 20190
## 182 17225 14246
## 183 17225 3979
## 184 17225 16749
## 185 17225 8790
## 186 17225 5036
## 187 17225 13640
## 188 17225 15628
## 189 17225 25700
## 190 17225 1465
## 191 17225 2812
## 192 17225 891
## 193 17225 9125
## 194 17225 12108
## 195 17225 586
## 196 17225 1190
## 197 17225 10274
## 198 17225 7697
## 199 17225 7012
## 200 17225 7809
## 201 17225 15551
## 202 17225 26223
## 203 17225 15236
## 204 17225 1345
## 205 17225 14421
## 206 17225 15756
## 207 17225 13472
## 208 17225 27000
## 209 17225 9659
## 210 17225 72
## 211 17225 29234
## 212 17225 11527
## 213 17225 9126
## 214 17225 7662
## 215 17225 17466
## 216 17225 29354
## 217 17225 5641
## 218 17225 1463
## 219 17225 643
## 220 17225 1215
## 221 17225 14927
## 222 17225 2814
## 223 17225 5058
## 224 17225 3055
## 225 17225 12214
## 226 17225 15260
## 227 17225 15258
## 228 17225 12281
## 229 17225 13099
## 230 17225 11448
## 231 17225 12283
## 232 17225 15679
## 233 17225 11518
## 234 17225 13098
## 235 17225 1218
## 236 17225 18616
## 237 17225 12107
## 238 17225 1322
## 239 17225 9668
## 240 17225 19316
## 241 17225 25698
## 242 17225 11533
## 243 17225 14785
## 244 17225 15140
## 245 17225 1587
## 246 17225 12105
## 247 17225 15517
## 248 17225 13309
## 249 17225 20282
## 250 17225 1139
## 251 17225 20278
## 252 17225 276
## 253 17225 239
## 254 17225 782
## 255 17225 969
## 256 17225 2030
## 257 17225 513
## 258 17225 3125
## 259 17225 789
## 260 17225 3544
## 261 17225 848
## 262 17225 238
## 263 17225 1236
## 264 17225 3851
## 265 17225 514
## 266 17225 2128
## 267 17225 1234
## 268 17225 849
## 269 17225 3576
## 270 17225 2050
## 271 17225 6238
## 272 17225 513
## 273 17225 1606
## 274 17225 9565
## 275 17225 6493
## 276 17225 1435
## 277 17225 4708
## 278 17225 11814
## 279 17225 1879
## 280 17225 5365
## 281 17225 1469
## 282 17225 4709
## 283 17225 5138
## 284 17225 1862
## 285 17225 980
## 286 17225 7877
## 287 17225 12203
## 288 17225 1911
## 289 17225 9612
## 290 17225 773
## 291 17225 1418
## 292 17225 3070
## 293 17225 3133
## 294 17225 8791
## 295 17225 1276
## 296 17225 9795
## 297 17225 317
## 298 17225 470
## 299 17225 469
## 300 17225 377
## 301 17225 465
## 302 17225 464
## 303 17225 422
## 304 17225 328
## 305 17225 240
## 306 17225 238
## 307 17225 306
## 308 17225 239
## 309 17225 266
## 310 17225 318
## 311 17225 416
## 312 17225 299
## 313 17225 476
## 314 17225 323
## 315 17225 419
## 316 17225 423
## 317 17225 437
## 318 17225 471
## 319 17225 468
## 320 17225 420
## 321 17225 418
## 322 17225 314
## 323 17225 433
## 324 17225 1
## 325 17225 235
## 326 17225 280
## 327 17225 1344
## 328 17225 463
## 329 17225 201
## 330 17225 111
## 331 17225 167
## 332 17225 661
## 333 17225 292
## 334 17225 1297
## 335 17225 317
## 336 17225 1298
## 337 17225 672
## 338 17225 460
## 339 17225 1219
## 340 17225 255
## 341 17225 461
## 342 17225 305
## 343 17225 495
## 344 17225 1249
## 345 17225 1416
## 346 17225 674
## 347 17225 462
## 348 17225 628
## 349 17225 494
## 350 17225 660
## 351 17225 82
## 352 17225 1652
## 353 17225 286
## 354 17225 924
## 355 17225 554
## 356 17225 441
## 357 17225 1711
## 358 17225 1385
## 359 17225 440
## 360 17225 953
## 361 17225 270
## 362 17225 1017
## 363 17225 553
## 364 17225 335
## 365 17225 824
## 366 17225 336
## 367 17225 114
## 368 17225 1367
## 369 17225 525
## 370 17225 2820
## 371 17225 2415
## 372 17225 2822
## 373 17225 3302
## 374 17225 2429
## 375 17225 1750
## 376 17225 1407
## 377 17225 1882
## 378 17225 37
## 379 17225 196
## 380 17225 1
## 381 17225 29
## 382 17225 141
## 383 17225 18
## 384 17225 166
## 385 17225 110
## 386 17225 170
## parents
## 1 CORUM:0000000
## 2 CORUM:0000000
## 3 GO:0002376, GO:0050896
## 4 GO:0008150
## 5 GO:0050851
## 6 GO:0002252
## 7 GO:0008150
## 8 GO:0006955, GO:0098542
## 9 GO:0002757, GO:0002768
## 10 GO:0002253, GO:0002764
## 11 GO:0002764, GO:0007166
## 12 GO:0006950
## 13 GO:0006952, GO:0051707
## 14 GO:0002455, GO:0006956
## 15 GO:0006897, GO:0006909, GO:0008037
## 16 GO:0007165, GO:0050776
## 17 GO:0006897, GO:0006909, GO:0099024
## 18 GO:0009605, GO:0009607
## 19 GO:0043207, GO:0044419
## 20 GO:0002376
## 21 GO:0010324
## 22 GO:0050896
## 23 GO:0050896
## 24 GO:0008150
## 25 GO:0002376, GO:0050778
## 26 GO:0001775, GO:0002376
## 27 GO:0009987
## 28 GO:0061024
## 29 GO:0006959, GO:0016064
## 30 GO:0002429
## 31 GO:0002443
## 32 GO:0002252, GO:0002253, GO:0006959
## 33 GO:0009617, GO:0098542
## 34 GO:0002684, GO:0006955, GO:0048584, GO:0050776
## 35 GO:0002376, GO:0002682, GO:0048518
## 36 GO:0051707
## 37 GO:0002682, GO:0006955, GO:0048583
## 38 GO:0048518, GO:0048583, GO:0050896
## 39 GO:0002682, GO:0045321, GO:0050865
## 40 GO:0045321
## 41 GO:0002376, GO:0050789
## 42 GO:0042113, GO:0051249
## 43 GO:0001775, GO:0050794
## 44 GO:0016192
## 45 GO:0046649
## 46 GO:0006955
## 47 GO:0006955
## 48 GO:0007154, GO:0009987, GO:0023052, GO:0050794, GO:0051716
## 49 GO:0002694, GO:0046649
## 50 GO:0002449, GO:0002460
## 51 GO:0002684, GO:0002694, GO:0045321, GO:0050867
## 52 GO:0042113, GO:0050864, GO:0051251
## 53 GO:0007165
## 54 GO:0019724
## 55 GO:0001775, GO:0048522, GO:0050865
## 56 GO:0008150
## 57 GO:0002250
## 58 GO:0009987
## 59 GO:0009987
## 60 GO:0002696, GO:0046649, GO:0051249
## 61 GO:0050789, GO:0050896
## 62 GO:0016192
## 63 GO:0009987, GO:0050896
## 64 GO:0050896
## 65 GO:0008150, GO:0050789
## 66 GO:0009987, GO:0048518, GO:0050794
## 67 GO:0008150
## 68 GO:0008150, GO:0065007
## 69 GO:0048870
## 70 GO:0006810
## 71
## 72 GO:0016043
## 73 GO:0009987
## 74 GO:0009605, GO:0048583
## 75 GO:0006952
## 76 GO:0009653, GO:0050793
## 77 GO:0007275, GO:0048856
## 78 GO:0009987, GO:0050789
## 79 GO:0032501, GO:0050789
## 80 GO:0002443, GO:0002697
## 81 GO:0008150
## 82 GO:0009605, GO:0032101, GO:0048584
## 83 GO:0009987
## 84 GO:0002376, GO:0016477
## 85 GO:0008150
## 86 GO:0009987
## 87 GO:0050900, GO:0060326
## 88 GO:0042221, GO:0042330
## 89 GO:0009605, GO:0040011
## 90 GO:0032501, GO:0048518, GO:0051239
## 91 GO:0002252, GO:0002682
## 92 GO:0050900
## 93 GO:0048856
## 94 GO:0009987, GO:0032502
## 95 GO:0006952, GO:0031347, GO:0048584
## 96 GO:0045321
## 97 GO:0006935, GO:0016477, GO:0070887
## 98 GO:0002252, GO:0002684, GO:0002697
## 99 GO:0032502, GO:0048856
## 100 GO:0048869
## 101 GO:0001525, GO:0022603, GO:1901342
## 102 GO:0002252, GO:0045055, GO:0051649
## 103 GO:0002429, GO:0002758
## 104 GO:1990840
## 105 GO:0009607
## 106 GO:0002220, GO:1990858
## 107 GO:0001944, GO:2000026
## 108 GO:0032502, GO:0050789
## 109 GO:0002520, GO:0048513
## 110 GO:0007165
## 111 GO:0006952, GO:0080134
## 112 GO:0001568, GO:0035239
## 113 GO:0032502
## 114 GO:0048534
## 115 GO:0001906, GO:0050794
## 116 GO:0048514, GO:0048646
## 117 GO:0051234
## 118 GO:0002218, GO:0002757
## 119 GO:0001906, GO:0002443
## 120 GO:0002697, GO:0043299, GO:1903305
## 121 GO:0007154, GO:0010646, GO:0048522
## 122 GO:0023051, GO:0023052, GO:0048518
## 123 GO:0007165, GO:0009966, GO:0010647, GO:0023056, GO:0048584
## 124 GO:0002376, GO:0048731
## 125 GO:0032501, GO:0048856
## 126 GO:0051179
## 127 GO:0010467, GO:0032501
## 128 GO:0050896
## 129 GO:0007155
## 130 GO:0030097, GO:0030154
## 131 GO:0002443
## 132 GO:0001944, GO:0048856
## 133 GO:0002263, GO:0045321
## 134 GO:0002228, GO:0002706, GO:0045088
## 135 GO:0097529
## 136 GO:0001775, GO:0002252, GO:0006955
## 137 GO:0001909, GO:0002703, GO:0031341
## 138 GO:0042221
## 139 GO:0001816, GO:0010468, GO:0051239
## 140 GO:0048731, GO:0072359
## 141 GO:0071621, GO:1990266
## 142 GO:0034097, GO:0045087
## 143 GO:0001910, GO:0002715, GO:0042267
## 144 GO:0007165, GO:0010646, GO:0023051, GO:0048583
## 145 GO:0050900
## 146 GO:0008150
## 147 GO:0016477, GO:2000145
## 148 GO:0001906, GO:0031341, GO:0048522
## 149 GO:0008219, GO:0010941, GO:0048522
## 150 GO:0007155, GO:0050794
## 151 GO:0042221, GO:0051716
## 152 GO:0009653, GO:0035295
## 153 GO:0030595, GO:0097530
## 154 GO:0065008
## 155 GO:0040011, GO:0050789
## 156 GO:0007165
## 157 GO:0097530
## 158 GO:0002274, GO:0002366
## 159 GO:0002449, GO:0045087
## 160 GO:0040012, GO:0048870, GO:0050794
## 161 GO:0023052, GO:0050789
## 162 GO:0002443, GO:0002699, GO:0002703
## 163 GO:0007154, GO:0050794
## 164 GO:0008283
## 165 GO:0042127, GO:0070661
## 166 GO:0002228, GO:0002708, GO:0002715, GO:0045089
## 167 GO:0065008
## 168 GO:0001909, GO:0002228
## 169 GO:0002274
## 170 GO:0050801
## 171 GO:0007155, GO:0030155, GO:0048522
## 172 GO:0002444, GO:0002703
## 173 GO:0009987
## 174 GO:0019932
## 175 GO:0009653
## 176 GO:0009611
## 177 GO:0048878
## 178 GO:0050801
## 179 GO:0065007
## 180 GO:0043085, GO:0051336
## 181 GO:0048731
## 182 GO:0032943, GO:0046649
## 183 GO:0006950
## 184 GO:0055080, GO:0098771
## 185 GO:0002237, GO:0033993, GO:1901700
## 186 GO:0010675, GO:0019220, GO:0031326, GO:0032958, GO:0043255, GO:1902930
## 187 GO:0001912, GO:0002717, GO:0042267, GO:0042269
## 188 GO:0008150
## 189 GO:0009967, GO:0035556, GO:1902531
## 190 GO:0002831, GO:0009607, GO:0048584
## 191 GO:0050801, GO:0055082
## 192 GO:0009617, GO:0010033, GO:0043207
## 193 GO:0070661
## 194 GO:0010942, GO:0012501, GO:0043067
## 195 GO:0001816, GO:0001817, GO:0010628, GO:0051240
## 196 GO:0030595, GO:0071674, GO:0097529
## 197 GO:0007275, GO:0048856
## 198 GO:0030097, GO:0030154
## 199 GO:0035556
## 200 GO:0016477, GO:0030334, GO:2000147
## 201 GO:0032502, GO:0048518, GO:0050793
## 202 GO:0002521
## 203 GO:0032944, GO:0046651, GO:0051249
## 204 GO:0002449, GO:0002703
## 205 GO:0006810
## 206 GO:0050790
## 207 GO:0001525, GO:0045765, GO:1904018
## 208 GO:0001944, GO:0051094, GO:0051240, GO:1901342
## 209 GO:0010033
## 210 GO:0035556
## 211 GO:0007275, GO:0050793, GO:0051239
## 212 GO:0036230
## 213 GO:0032943, GO:0070663
## 214 GO:0006873, GO:0055080
## 215 GO:0010676, GO:0010919, GO:0031328, GO:0032958, GO:0045937, GO:1902932
## 216 GO:0040017, GO:0048522, GO:0048870, GO:2000145
## 217 GO:0071840
## 218 GO:0009607, GO:0048583
## 219 GO:0001909, GO:0001910, GO:0002705, GO:0031343
## 220 GO:0002521, GO:0030099
## 221 GO:0009653, GO:0032502
## 222 GO:0030003, GO:0055065
## 223 GO:0008219, GO:0050794
## 224 GO:0098609
## 225 GO:0002699, GO:0043299, GO:0043300, GO:1903307
## 226 GO:0006954, GO:0031349, GO:0032103, GO:0050727
## 227 GO:0006954, GO:0031347, GO:0032101
## 228 GO:0000165, GO:1902531
## 229 GO:0002833, GO:0031349, GO:0032103, GO:0045087, GO:0045088, GO:0050778
## 230 GO:0040011, GO:0040012, GO:0048518
## 231 GO:0000165, GO:0043408, GO:1902533
## 232 GO:0032501, GO:0048519, GO:0051239
## 233 GO:0042113, GO:0046651
## 234 GO:0002831, GO:0031347, GO:0032101, GO:0045087, GO:0050776
## 235 GO:0045055, GO:0051649
## 236 GO:0019221, GO:1990869
## 237 GO:0010941, GO:0012501
## 238 GO:0002376, GO:0002682, GO:0048519
## 239 GO:0098609
## 240 GO:0010033, GO:0070887
## 241 GO:0009966, GO:0035556
## 242 GO:0008283, GO:0050794
## 243 GO:0030154, GO:0048856, GO:0048869
## 244 GO:0032501, GO:0042592
## 245 GO:0003008
## 246 GO:0006915, GO:0042981, GO:0043068
## 247 GO:0046903, GO:0051049
## 248 GO:0030154, GO:0045595, GO:0048522, GO:0051094
## 249 GO:0055080, GO:0098771
## 250 GO:0002504, GO:0048002
## 251 GO:0030003, GO:0072507
## 252 GO:0005576, GO:0110165
## 253 GO:0110165
## 254 GO:0005886, GO:0009986, GO:0098552
## 255 GO:0032991
## 256 GO:0005615, GO:0019814
## 257 GO:0016020, GO:0071944
## 258 GO:0110165
## 259 GO:0110165
## 260 GO:0016020, GO:0110165
## 261 GO:0110165
## 262
## 263 GO:0005886, GO:0031224
## 264 GO:0005575
## 265 GO:0016021, GO:0031226
## 266 GO:0032991
## 267 GO:0016020, GO:0110165
## 268 GO:0031224
## 269 GO:0005886, GO:0016020
## 270 GO:0042611
## 271 GO:0005102
## 272 GO:0005488
## 273 GO:0005515
## 274 GO:0003674
## 275 GO:0060089
## 276 GO:0038023
## 277 GO:0044877
## 278 GO:0038023
## 279 GO:0005488
## 280 GO:0004888, GO:0140375
## 281 GO:0004888
## 282 GO:0023023
## 283 GO:0048020
## 284 GO:0003674
## 285 HP:0011450
## 286 HP:0002011, HP:0032158
## 287 HP:0032101
## 288 HP:0033353
## 289 HP:0000118
## 290 HP:0011123
## 291 HP:0004370
## 292 HP:0012337
## 293 HP:0004447
## 294 HP:0025142
## 295 HP:0003271, HP:0025408
## 296 HP:0008047
## 297 KEGG:00000
## 298 KEGG:00000
## 299 KEGG:00000
## 300 KEGG:00000
## 301 KEGG:00000
## 302 KEGG:00000
## 303 KEGG:00000
## 304 KEGG:00000
## 305 KEGG:00000
## 306 KEGG:00000
## 307 KEGG:00000
## 308 KEGG:00000
## 309 KEGG:00000
## 310 KEGG:00000
## 311 KEGG:00000
## 312 KEGG:00000
## 313 KEGG:00000
## 314 KEGG:00000
## 315 KEGG:00000
## 316 KEGG:00000
## 317 KEGG:00000
## 318 KEGG:00000
## 319 KEGG:00000
## 320 KEGG:00000
## 321 KEGG:00000
## 322 KEGG:00000
## 323 KEGG:00000
## 324
## 325 KEGG:00000
## 326 MIRNA:000000
## 327 REAC:R-MMU-2173782
## 328 REAC:R-MMU-2029480
## 329 REAC:R-MMU-983705
## 330 REAC:R-MMU-983705
## 331 REAC:R-MMU-5653656
## 332 REAC:R-MMU-1280218
## 333 REAC:R-MMU-166786
## 334 REAC:R-MMU-2454202
## 335 REAC:R-MMU-166663
## 336 REAC:R-MMU-2029480
## 337 REAC:R-MMU-166658
## 338 REAC:R-MMU-2454202
## 339 REAC:R-MMU-166658
## 340 REAC:R-MMU-109582
## 341 REAC:R-MMU-2454202
## 342 REAC:R-MMU-168249
## 343 REAC:R-MMU-168249
## 344 REAC:R-MMU-2029480
## 345 REAC:R-MMU-1280218
## 346 REAC:R-MMU-168256
## 347 REAC:R-MMU-2454202
## 348 REAC:0000000
## 349 REAC:R-MMU-168249
## 350 REAC:0000000
## 351 REAC:R-MMU-168256
## 352 REAC:0000000
## 353 REAC:R-MMU-500792
## 354 REAC:R-MMU-168249
## 355 REAC:R-MMU-372790
## 356 REAC:R-MMU-1480926
## 357
## 358 REAC:R-MMU-162582
## 359 REAC:R-MMU-1480926
## 360 REAC:R-MMU-382551
## 361 REAC:R-MMU-375276
## 362 REAC:R-MMU-373076
## 363 REAC:R-MMU-372790
## 364 REAC:R-MMU-168249
## 365 REAC:R-MMU-6803157
## 366 REAC:R-MMU-2172127
## 367 REAC:R-MMU-168249
## 368 REAC:0000000
## 369 REAC:R-MMU-388396
## 370 TF:M00000
## 371 TF:M01808
## 372 TF:M00000
## 373 TF:M00000
## 374 TF:M07107
## 375 TF:M00000
## 376 TF:M00192
## 377 TF:M00000
## 378 WP:000000
## 379 WP:000000
## 380
## 381 WP:000000
## 382 WP:000000
## 383 WP:000000
## 384 WP:000000
## 385 WP:000000
## 386 WP:000000# what are our outputs # plot our results using in built function in g:profiler -> which one is it?
gostplot(
gostres = gost_results_obj,
capped = TRUE,
interactive = TRUE,
pal = c(`GO:MF` = "#dc3912", `GO:BP` = "#ff9900", `GO:CC` = "#109618", KEGG =
"#dd4477", REAC = "#3366cc", WP = "#0099c6", TF = "#5574a6", MIRNA = "#22aa99", HPA =
"#6633cc", CORUM = "#66aa00", HP = "#990099")
)# what does as_short_link = FALSE do in gost() function?
gost_results_obj_sl <- gost(
query = upreg_gene_ids,
organism = "mmusculus",
exclude_iea = TRUE,
as_short_link = TRUE,
correction_method = c("g_SCS"),
custom_bg = all_gene_ids,
)## Detected custom background input, domain scope is set to 'custom'gost_results_obj_sl## [1] "https://biit.cs.ut.ee/gplink/l/yb6BZAz7QW"Answer ->
# Filter results table for genesets with between 5-300 genes Can you plot these querys together?
Output the get_version_info() to save the versions of the databases that were used for the analysis!!
Output the sessionInfo() so know what packages we used
sessionInfo()## R version 4.2.1 (2022-06-23)
## Platform: x86_64-apple-darwin17.0 (64-bit)
## Running under: macOS Big Sur ... 10.16
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] gprofiler2_0.2.1 forcats_0.5.2 stringr_1.4.1 dplyr_1.0.10
## [5] purrr_0.3.5 readr_2.1.3 tidyr_1.2.1 tibble_3.1.8
## [9] ggplot2_3.4.0 tidyverse_1.3.2
##
## loaded via a namespace (and not attached):
## [1] httr_1.4.4 sass_0.4.2 jsonlite_1.8.3
## [4] viridisLite_0.4.1 modelr_0.1.9 bslib_0.4.1
## [7] shiny_1.7.3 assertthat_0.2.1 googlesheets4_1.0.1
## [10] cellranger_1.1.0 yaml_2.3.6 pillar_1.8.1
## [13] backports_1.4.1 glue_1.6.2 digest_0.6.30
## [16] promises_1.2.0.1 rvest_1.0.3 colorspace_2.0-3
## [19] htmltools_0.5.3 httpuv_1.6.6 pkgconfig_2.0.3
## [22] broom_1.0.1 haven_2.5.1 xtable_1.8-4
## [25] scales_1.2.1 later_1.3.0 tzdb_0.3.0
## [28] timechange_0.1.1 googledrive_2.0.0 generics_0.1.3
## [31] ellipsis_0.3.2 cachem_1.0.6 withr_2.5.0
## [34] lazyeval_0.2.2 cli_3.4.1 magrittr_2.0.3
## [37] crayon_1.5.2 readxl_1.4.1 mime_0.12
## [40] evaluate_0.18 fs_1.5.2 fansi_1.0.3
## [43] xml2_1.3.3 tools_4.2.1 data.table_1.14.4
## [46] hms_1.1.2 gargle_1.2.1 lifecycle_1.0.3
## [49] plotly_4.10.1 munsell_0.5.0 reprex_2.0.2
## [52] compiler_4.2.1 jquerylib_0.1.4 rlang_1.0.6
## [55] grid_4.2.1 RCurl_1.98-1.9 rstudioapi_0.14
## [58] htmlwidgets_1.5.4 crosstalk_1.2.0 bitops_1.0-7
## [61] rmarkdown_2.18 gtable_0.3.1 DBI_1.1.3
## [64] R6_2.5.1 lubridate_1.9.0 knitr_1.40
## [67] fastmap_1.1.0 utf8_1.2.2 stringi_1.7.8
## [70] Rcpp_1.0.9 vctrs_0.5.0 dbplyr_2.2.1
## [73] tidyselect_1.2.0 xfun_0.34Now knit your report to get a lovely html file that you can share -> this is good practise as it creates a permanent record of your plots/analysis output and also makes sure your script runs without error from start to finish!